{ "type": "genome", "identifier": "GCA_020721685.1", "organism": "Paludibacter propionicigenes", "title": "Paludibacter propionicigenes", "description": "derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "University Duisburg-Essen", "publication": [ {} ], "properties": { "assembly_accession": "GCA_020721685.1", "bioproject": "PRJNA767587", "biosample": "SAMN22209467", "wgs_master": "DYMF00000000.1", "refseq_category": "na", "taxid": "185300", "species_taxid": "185300", "organism_name": "Paludibacter propionicigenes", "infraspecific_name": "", "isolate": "SulCav_FS06-10_38_37", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/11/02", "asm_name": "ASM2072168v1", "submitter": "University Duisburg-Essen", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/020/721/685/GCA_020721685.1_ASM2072168v1", "excluded_from_refseq": "derived from metagenome", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-11-02", "dateModified": "2021-11-02", "datePublished": "2021-11-02", "_annotation": { "sample_count": 1, "sample_organism": [ "Paludibacter propionicigenes" ], "sample_taxid": [ "185300" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Italy: Frasassi cave" ], "sample_host_location_id": [], "data_size": "0.572 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 79.17, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "2010357", "Number of Sequences": "140", "Longest Sequences (bp)": "58693", "N50 (bp)": "18565", "Gap Ratio (%)": "0.383017", "GCcontent (%)": "37.9", "Number of CDSs": "1518", "Average Protein Length": "369.6", "Coding Ratio (%)": "83.7", "Number of rRNAs": "0", "Number of tRNAs": "17", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Paludibacter propionicigenes", "strain": "strain=WB4", "accession": "GCA_000183135.1", "taxid": 185300, "species_taxid": 185300, "relation_to_type": "type", "validated": true, "ani": 77.5312, "matched_fragments": 83, "total_fragments": 596, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 79.17, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_903912795.1", "gtdb_species": "s__Paludibacter sp903912795", "ani": 79.3437, "matched_fragments": 211, "total_fragments": 596, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCA_017989795.1", "gtdb_species": "s__Paludibacter sp017989795", "ani": 78.4603, "matched_fragments": 120, "total_fragments": 596, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCA_018054805.1", "gtdb_species": "s__Paludibacter sp018054805", "ani": 77.9551, "matched_fragments": 65, "total_fragments": 596, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCA_001873635.1", "gtdb_species": "s__Paludibacter sp001873635", "ani": 77.7202, "matched_fragments": 133, "total_fragments": 596, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCA_016937795.1", "gtdb_species": "s__Paludibacter sp016937795", "ani": 77.6726, "matched_fragments": 116, "total_fragments": 596, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCA_009929375.1", "gtdb_species": "s__Paludibacter sp009929375", "ani": 77.6647, "matched_fragments": 136, "total_fragments": 596, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCA_002427615.1", "gtdb_species": "s__Paludibacter sp002427615", "ani": 77.631, "matched_fragments": 126, "total_fragments": 596, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.75", "min_intra_species_ani": "99.75", "mean_intra_species_af": "0.80", "min_intra_species_af": "0.80", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_903873355.1", "gtdb_species": "s__Paludibacter sp903873355", "ani": 77.5169, "matched_fragments": 71, "total_fragments": 596, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCA_013426815.1", "gtdb_species": "s__Paludibacter sp013426815", "ani": 77.4095, "matched_fragments": 81, "total_fragments": 596, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCA_019163375.1", "gtdb_species": "s__Paludibacter sp019163375", "ani": 77.3534, "matched_fragments": 98, "total_fragments": 596, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCA_017882285.1", "gtdb_species": "s__Paludibacter sp017882285", "ani": 77.3134, "matched_fragments": 103, "total_fragments": 596, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCA_010365115.1", "gtdb_species": "s__Paludibacter sp010365115", "ani": 77.2838, "matched_fragments": 115, "total_fragments": 596, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCA_903830915.1", "gtdb_species": "s__Paludibacter sp903830915", "ani": 77.1846, "matched_fragments": 92, "total_fragments": 596, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCA_017860345.1", "gtdb_species": "s__Paludibacter sp017860345", "ani": 76.6749, "matched_fragments": 87, "total_fragments": 596, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCA_015654525.1", "gtdb_species": "s__Paludibacter sp015654525", "ani": 76.584, "matched_fragments": 82, "total_fragments": 596, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.302, "cell_length": 0.113, "doubling_h": null, "growth_tmp": 25.0, "optimum_tmp": 30.0, "optimum_ph": 6.6, "genome_size": 3685503.2, "gc_content": 39.1, "coding_genes": 2985.333, "rRNA16S_genes": 3.0, "tRNA_genes": 53.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 1.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_gtdb_taxon": [ "d__Bacteria", "p__Bacteroidota", "c__Bacteroidia", "o__Bacteroidales", "f__Paludibacteraceae", "g__Paludibacter", "s__Paludibacter sp020726365" ], "_genome_taxon": [ "Paludibacter", "propionicigenes", "d__Bacteria", "p__Bacteroidota", "c__Bacteroidia", "o__Bacteroidales", "f__Paludibacteraceae", "g__Paludibacter", "s__Paludibacter sp020726365", "Bacteria", "Bacteroidota", "Bacteroidia", "Bacteroidales", "Paludibacteraceae", "Paludibacter", "Paludibacter", "sp020726365" ], "_meo": [ { "id": "MEO_0000366", "label": "ground water" }, { "id": "MEO_0000116", "label": "biofilm" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }